PAH-DNA

Genotoxicity of PAH-DNA adducts

Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) software is used to run molecular dynamics simulations and free energy perturbations.

User guides:
NAMD: Unix/Mac or Windows
VMD

File Explanations:

equil_scripts

These scripts are needed for preparation of the system to undergo simulations.
The order is significant.

1. Minimize the system to ensure reasonable atom positions
   file: min2.namd
   

2. Relax the backbone and water box in the system, while also maintaining shape.
   file 1: equilNVT2.namd
   file 2: equilNPT2.namd
   

3. Shape water box for most stable box possible, minimizing surface tension
   file: equilibrate_IA2.namd
   

4. Run FEP forwards and backwards.
   file 1: forward_IA-on3.namd
   file 2: backward_IA-on3.namd
   

Toppar
Topology files defining bonds between atoms.

README and this repository are still in progress.